The 5-speed is defiantly the way to go.  Every time I drive my car I'm glad we did it.  I'll give you some details about what I learned doing mine.

        First off, what you want is a Borg-Warner T-5 out of a fox body mustang.  There are three kinds of this tranny.  I don't know what the first year of the early T-5 was but they were in cars until '84.  All the mustang magazines say this is the one not to get because it is supposed to be a lot weaker than the later ones.
My T-5 transmission in all of it's glory
        In '85-'89 the transmissions got better gears and synchros and were stronger than the early ones.  They also came from the factory with a shorter throw shifter than the early or late trannys. The other feature of this generation is that it has a 3.35:1 first gear.  The tranny in my car is out of an '89 because that is what I found in the newspaper.

        The later trannys were in cars from '90-'93 these are the so called "world class" T-5's and they are even stronger than the middle year trannys.  However their shifter is a longer throw than the middle year trannys.  These trannys can be identified because the shifter assembly has that gold cadmium plating on it where the shifters from the other years were black

       "All ford world class stock boxes are 3.35.  Everything from 85 on are "world class".  90-93 are strong because of higher nickel in the steel.  World class means carbon fiber lined synros and tapered bearings on the lower cluster. There also are roller bearing under each gear.  A non-world class box can not be upgraded and had 2.95 gear sets." - Bruce

        You can't put a transmission from a '94 or later car in without changing some parts.

        "The input shaft and bearing retain are the only changes need to made it a 93 spec tranny." - Bruce

        The moral of the story is that you want a tranny from an '85-'93 car. And since after market shifters are so incredibly expensive for these trannys it might be worth your time to find a '85-'89 shifter if you get a '90-'93 transmission.  The tranny by itself should cost about $350 out of some one's back yard.

        This brings us to putting the transimssion in the car.  a T-5 has a longer input shaft than a ford transmission from the 60's to accommodate this you have to have a deeper bell housing   However the spline and pilot bearing diameter on the input shaft are the same as the old transmissions.

        The best way to attach the transmission to the engine is to use a T-5 bell housing  (You can put an adapter plate on an old bell housing but it costs a lot $$$$.)  Since the T-5 bell housing is designed for a cable clutch you have to modify it to work with the older style clutch.  (You can get kits to put a cable clutch linkage in an early car but this also costs $$$$.)
This is the spacer viewed through the clutch fork window

The two flush allen head bolts attach the spacer bolk and clutch fork pivot
        This involves putting a spacer on the floor of the bell housing to mount the early-style clutch pivot.  The spacer should raise the pivot 1" away from the floor of the bell housing  I've also seen 3/4" spacers used, so you should be safe anywhere between those two lengths, you just have to make up the difference in the clutch linkage.  The two holes to mount it should be drilled about 1.5" away from where the floor of the bell housing ends at the window for the release arm. You should also take the pivot for the cable style clutch off.
Sorry for the big file, and its not to scale.
        On the crossmember and transmission mount, You'll should probably just buy a crossmember.  Any Mustang catalog should have one.  For the mount all ford transmissions, automatic and manual, from some time in the 50's to I think 1973 used the same transmission mount.  That's the mount you want.  It shouldn't be too hard to find.
The cross member, make sure you get one with an E-brake bracket
        Now we get to what clutch parts to use.  You should probably use an early clutch, just get the one for your car.  The input shaft will go right into the early clutch and pilot bearing.  You also use the early release arm and throwout bearing.

        If you build an engine you can put a late style clutch on.  To use a late style clutch you also have to use a late style flywheel.  Remember that before '82 small fords had a 28.8oz external counterbalance and after '82 they had a 50oz counterbalance so you can't just put a late flywheel on an early engine.  If you do use a later style clutch you still use the early release arm and throwout bearing.

        You might need to cut and shorten the little bar that pushes on the release arm like I had to if the clutch ends up out of the adjustment range.  Interestingly, when I later changed the clutch, the shortened bar was too short, so I bought an adjustable length clutch pushrod for a '66 mustang with a v8 and make the linkage work the way I wanted it to.
My modified push rod.

The adjustable length pushrod
        On flywheels, ford had two sizes for smallblocks.  You have to have a 157 tooth flywheel as a 164 tooth flywheel will not fit in the T-5 bell housing  All 289's and all late small blocks have the 157 tooth flywheel.  However some early 302's and 351's had the bigger flywheel.

        The back up light switch on the T-5 worked exactly the same as the one on my three speed, it connects the two terminals of the switch when the shifter is put into reverse.  I cut the wires off of the old switch, lengthened them, and since I didn't have the special connector, I modified two male bullet connectors to go over the switch terminals.
My back up light wiring, note the creative use of crimp connectors
        As far as drive-shafts go the T-5 is slightly longer than the early transmission and you will almost certainly have to have the drive-shaft shortened.  If you want to get a slip yolk from the junkyard you can use one from any T-5 or AOD (automatic overdrive) transmission.  Otherwise the drive-shaft guy will sell you a slip yolk.

        The speedometer hooks straight up, you just pop the cable from the car into the new tranny and it should read accurately.  If it doesn't, get a ford motorsport catalog because it will tell you how many teeth the seedo drive gear in the transmission has. Then you can use the formula and buy the right driven gear for the car.  (I used to know how many teeth the drive gear should have but I'm writing this all from memory and I can't remember everything.)

        The shifter on the T-5 ends up about an inch forward of where the old shifter went.  This shouldn't pose a problem unless you have a console like me.  The T-5 shifter has a stub shaft with two threaded holes so just do what I did and get a $5 chrome hurst lever from a swap meet, cut the end off, drill two holes and have a good day.  Hurst now has a five speed knob that looks perfect, I bought one, annoyingly you can't order from Hurst's catalog, you have to find a shop to order the part if it isn't in stock
Can you say FIVE SPEED?
        You'll probably have to fight with the e-brake a little but it shouldn't be too bad.  I had to get a longer threaded adjuster bar to work with my rear disc brakes and I had to bend the E-brake pivot bar to clear my exhaust because the E-brake bracket was at a different height on the new cross member

        Well, that's about all there is to it, It sounds like a lot but once you have all the stuff the swap is just like changing a clutch (if you don't know how to change a clutch ask someone to help you do the transmission swap)

        Here's what it looks like all together, how bitchen.
Isn't that cool?

        If you found this usefull, or know of anything I need to add or clarify please email me.

        Special thanks to Bruce "The T-5 guy" Couture for a few corrections